Variant report

Variant	rs62175449
Chromosome Location	chr2:179990211-179990212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:179989101-179991030	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SESTD1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12622222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866609	1.00[AFR][1000 genomes]
rs17363057	1.00[AFR][1000 genomes]
rs17454087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17454527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62175447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175448	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62175450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62177277	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62177281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177291	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62177326	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177327	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62177339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62179066	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62179067	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62179068	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62179069	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
2	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
4	chr2:179971600-179991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:179972600-180001800	Weak transcription	NHEK	skin
9	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
11	chr2:179973400-180004400	Weak transcription	Pancreas	Pancrea
12	chr2:179973400-180006800	Weak transcription	Small Intestine	intestine
13	chr2:179973400-180012600	Weak transcription	NHLF	lung
14	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:179974400-179994200	Strong transcription	HepG2	liver
16	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:179976000-180004400	Weak transcription	Aorta	Aorta
18	chr2:179977400-180004400	Weak transcription	Lung	lung
19	chr2:179977400-180005000	Weak transcription	Fetal Kidney	kidney
20	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
21	chr2:179977600-180002000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:179978800-180004400	Weak transcription	Spleen	Spleen
24	chr2:179980000-180038800	Weak transcription	HMEC	breast
25	chr2:179980000-180056800	Weak transcription	HSMM	muscle
26	chr2:179980400-180005200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:179980400-180005600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:179981000-179991000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:179981400-180001800	Weak transcription	Placenta	Placenta
30	chr2:179981400-180005000	Weak transcription	Ovary	ovary
31	chr2:179981400-180016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:179981600-179991000	Weak transcription	Brain Anterior Caudate	brain
33	chr2:179981600-179997600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:179981600-180004400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:179981600-180005000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:179981800-180005400	Weak transcription	Osteobl	bone
37	chr2:179982400-180004400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:179982800-180004400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:179982800-180004600	Weak transcription	Fetal Brain Male	brain
40	chr2:179983600-180005000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:179984600-180003000	Weak transcription	Fetal Lung	lung
42	chr2:179984600-180004600	Weak transcription	HUVEC	blood vessel
43	chr2:179984800-180002000	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:179984800-180004200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:179984800-180005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:179985000-180025600	Weak transcription	Fetal Intestine Small	intestine
47	chr2:179985200-180004400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:179985200-180004400	Weak transcription	Fetal Stomach	stomach
49	chr2:179985400-180004000	Weak transcription	Dnd41	blood
50	chr2:179985600-179996200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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